Publication Date
2007
Journal or Book Title
PLoS ONE
Abstract
Background
SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli. A time series microarray design was used to identify co-regulated SoxRS-dependent and independent genes modulated by superoxide minutes after exposure to stress.
Methodology/Principal Findings
soxS mRNA levels surged to near maximal levels within the first few minutes of exposure to paraquat, a superoxide-producing compound, followed by a rise in mRNA levels of known SoxS-regulated genes. Based on a new method for determining the biological significance of clustering results, a total of 138 genic regions, including several transcription factors and putative sRNAs were identified as being regulated through the SoxRS signaling pathway within 10 minutes of paraquat treatment. A statistically significant two-block SoxS motif was identified through analysis of the SoxS-regulated genes. The SoxRS-independent response included members of the OxyR, CysB, IscR, BirA and Fur regulons. Finally, the relative sensitivity to superoxide was measured in 94 strains carrying deletions in individual, superoxide-regulated genes.
Conclusions/Significance
By integrating our microarray time series results with other microarray data, E. coli databases and the primary literature, we propose a model of the primary transcriptional response containing 226 protein-coding and sRNA sequences. From the SoxS dependent network the first statistically significant SoxS-related motif was identified.
DOI
https://doi.org/10.1371/journal.pone.0001186
Volume
2
Issue
11
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Recommended Citation
Blanchard, Jeffrey L.; Wholey, Wei-Yun; Conlon, Erin M.; and Pomposiello, Pablo J., "Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks" (2007). PLoS ONE. 2.
https://doi.org/10.1371/journal.pone.0001186